core ID: scRNA_00
Report Version: 1.0
Request by: Jonathan Baldan ()
Principal Investigator: Luis Arnes ()
Organisation: BRIC
core Staff: Juliana Assis ()


1 Setup

All libraries/packages

2 Background

The study consist of 21 Mice  

2.1 Data

There are 21 Mice and 7 samples

  • Type of data
    scRNA

  • Data location
    Lehmann

  • Reference data used Mouse

3 Explanation of the Report

The report is divided into two parts: methods and results. In the results section, it is also possible to find more explanations. It is possible to download all plots and tables by clicking copy/save.

4 Methods

Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics’ Single-Cell Gene Expression Software Cell Ranger version 7.2.0 (“mkfastq” pipeline, default parameters) Ref1.

The nf-core sc-rnaseq pipeline, version 2.4.1 Ref2, was selected to perform a best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. 10x Genomics provided the reference genome sequenced: Mouse reference (mm10) - 2020-A Ref3.

Filtered gene expression matrices were then analysed using Scarfweb Ref4 and Ref5. Individual analyses for each sample were performed for quality control. Poor-quality cells were filtered using the auto_filter_cells function using default values Ref4. In addition, all cells with >20% mitochondrial counts were removed.